BACKGROUND: The efficacy of rabeprazole 5 mg/day for patients with non-erosive reflux disease (NERD) has not been reported in the literature. AIM: To evaluate the efficacy of rabeprazole 5 mg and 10 mg/day in Japanese NERD patients. The influence of baseline characteristics as well as genetic background on efficacy was also analysed. METHODS: Subjects were grade M (minimal changes) NERD patients. Two hundred and eighty-eight of these subjects, who were nonresponders to open label antacid therapy, entered in a 4-week, double-blind treatment (placebo, rabeprazole 5 mg or 10 mg/day). RESULTS: Complete heartburn relief rates were 21% in placebo, 34% in rabeprazole 5 mg and 44% in rabeprazole 10 mg (5 mg vs. placebo P = 0.074, 10 mg vs. placebo P = 0.001). Rabeprazole 5 mg was significantly more effective than placebo in elderly patients and in patients with low heartburn frequency or without hiatal hernia. The efficacy of rabeprazole 10 mg was not influenced by age, BMI, hiatal hernia, Helicobacter pylori infection, frequency and severity of heartburn or CYP2C19 genotypes. CONCLUSIONS: Rabeprazole 5 mg was effective in a subgroup of Japanese NERD patients. Rabeprazole 10 mg provided more potent heartburn relief than 5 mg and was less fragile to baseline characteristics.